7ARW

Structure of human ARH3 E41A bound to alpha-NAD+ and magnesium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Mechanistic insights into the three steps of poly(ADP-ribosylation) reversal.

Rack, J.G.M.Liu, Q.Zorzini, V.Voorneveld, J.Ariza, A.Honarmand Ebrahimi, K.Reber, J.M.Krassnig, S.C.Ahel, D.van der Marel, G.A.Mangerich, A.McCullagh, J.S.O.Filippov, D.V.Ahel, I.

(2021) Nat Commun 12: 4581-4581

  • DOI: https://doi.org/10.1038/s41467-021-24723-3
  • Primary Citation of Related Structures:  
    7AKR, 7AKS, 7AQM, 7ARW

  • PubMed Abstract: 

    Poly(ADP-ribosyl)ation (PAR) is a versatile and complex posttranslational modification composed of repeating units of ADP-ribose arranged into linear or branched polymers. This scaffold is linked to the regulation of many of cellular processes including the DNA damage response, alteration of chromatin structure and Wnt signalling. Despite decades of research, the principles and mechanisms underlying all steps of PAR removal remain actively studied. In this work, we synthesise well-defined PAR branch point molecules and demonstrate that PARG, but not ARH3, can resolve this distinct PAR architecture. Structural analysis of ARH3 in complex with dimeric ADP-ribose as well as an ADP-ribosylated peptide reveal the molecular basis for the hydrolysis of linear and terminal ADP-ribose linkages. We find that ARH3-dependent hydrolysis requires both rearrangement of a catalytic glutamate and induction of an unusual, square-pyramidal magnesium coordination geometry.


  • Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribose glycohydrolase ARH3
A, B
349Homo sapiensMutation(s): 1 
Gene Names: ADPRSADPRHL2ARH3
EC: 3.5.1 (PDB Primary Data), 3.2.1.143 (PDB Primary Data), 3.2.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NX46 (Homo sapiens)
Explore Q9NX46 
Go to UniProtKB:  Q9NX46
PHAROS:  Q9NX46
GTEx:  ENSG00000116863 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NX46
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8NA (Subject of Investigation/LOI)
Query on 8NA

Download Ideal Coordinates CCD File 
E [auth A],
O [auth B]
alpha-Diphosphopyridine nucleotide
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-OPDHFMQKSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
J [auth A]
K [auth A]
F [auth A],
G [auth A],
H [auth A],
J [auth A],
K [auth A],
L [auth A],
P [auth B],
Q [auth B],
R [auth B],
T [auth B],
U [auth B],
V [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
I [auth A],
S [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
M [auth B],
N [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.746α = 115.8
b = 66.112β = 94.98
c = 70.055γ = 104.07
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom101794
Wellcome TrustUnited Kingdom210634

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-16
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description